Starting phenix.real_space_refine on Mon Aug 25 22:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdm_17614/08_2025/8pdm_17614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdm_17614/08_2025/8pdm_17614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2025/8pdm_17614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2025/8pdm_17614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2025/8pdm_17614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2025/8pdm_17614.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 121 5.16 5 C 19602 2.51 5 N 5445 2.21 5 O 6226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31471 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 3.23, per 1000 atoms: 0.10 Number of scatterers: 31471 At special positions: 0 Unit cell: (199.5, 200.55, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 77 15.00 O 6226 8.00 N 5445 7.00 C 19602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 876.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 22 sheets defined 68.4% alpha, 2.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 141 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 141 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 361 Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 141 Processing helix chain 'G' and resid 156 through 170 Processing helix chain 'G' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'I' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 141 Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 361 Processing helix chain 'K' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR K 13 " --> pdb=" O SER K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 141 Processing helix chain 'K' and resid 156 through 170 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 361 Processing helix chain 'M' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR M 13 " --> pdb=" O SER M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU M 46 " --> pdb=" O GLN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 141 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 175 through 191 removed outlier: 4.032A pdb=" N ARG M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS M 283 " --> pdb=" O GLN M 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR O 13 " --> pdb=" O SER O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU O 46 " --> pdb=" O GLN O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 120 through 141 Processing helix chain 'O' and resid 156 through 170 Processing helix chain 'O' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG O 189 " --> pdb=" O ARG O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 198 Processing helix chain 'O' and resid 202 through 217 Processing helix chain 'O' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER O 222 " --> pdb=" O VAL O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 251 Processing helix chain 'O' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG O 260 " --> pdb=" O GLN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 274 Processing helix chain 'O' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS O 283 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY O 300 " --> pdb=" O PRO O 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 297 through 300' Processing helix chain 'O' and resid 318 through 332 Processing helix chain 'O' and resid 344 through 361 Processing helix chain 'Q' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR Q 13 " --> pdb=" O SER Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 141 Processing helix chain 'Q' and resid 156 through 170 Processing helix chain 'Q' and resid 175 through 191 removed outlier: 4.034A pdb=" N ARG Q 189 " --> pdb=" O ARG Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 198 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER Q 222 " --> pdb=" O VAL Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 251 Processing helix chain 'Q' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG Q 260 " --> pdb=" O GLN Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 274 Processing helix chain 'Q' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY Q 300 " --> pdb=" O PRO Q 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 297 through 300' Processing helix chain 'Q' and resid 318 through 332 Processing helix chain 'Q' and resid 344 through 361 Processing helix chain 'S' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR S 13 " --> pdb=" O SER S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU S 46 " --> pdb=" O GLN S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 141 Processing helix chain 'S' and resid 156 through 170 Processing helix chain 'S' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG S 189 " --> pdb=" O ARG S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 251 Processing helix chain 'S' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 Processing helix chain 'S' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS S 283 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'U' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR U 13 " --> pdb=" O SER U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU U 46 " --> pdb=" O GLN U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 75 Processing helix chain 'U' and resid 75 through 86 Processing helix chain 'U' and resid 120 through 141 Processing helix chain 'U' and resid 156 through 170 Processing helix chain 'U' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG U 189 " --> pdb=" O ARG U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 198 Processing helix chain 'U' and resid 202 through 217 Processing helix chain 'U' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER U 222 " --> pdb=" O VAL U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 251 Processing helix chain 'U' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG U 260 " --> pdb=" O GLN U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 270 through 274 Processing helix chain 'U' and resid 275 through 296 removed outlier: 4.527A pdb=" N LYS U 283 " --> pdb=" O GLN U 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN U 284 " --> pdb=" O ALA U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY U 300 " --> pdb=" O PRO U 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 297 through 300' Processing helix chain 'U' and resid 318 through 332 Processing helix chain 'U' and resid 344 through 361 Processing sheet with id=1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG C 96 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR E 33 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG E 96 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'G' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG G 96 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR I 33 " --> pdb=" O VAL I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG I 96 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR K 33 " --> pdb=" O VAL K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG K 96 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'M' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG M 96 " --> pdb=" O ASP M 115 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'O' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR O 33 " --> pdb=" O VAL O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'O' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG O 96 " --> pdb=" O ASP O 115 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Q' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR Q 33 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG Q 96 " --> pdb=" O ASP Q 115 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'S' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'S' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG S 96 " --> pdb=" O ASP S 115 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'U' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR U 33 " --> pdb=" O VAL U 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'U' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG U 96 " --> pdb=" O ASP U 115 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10136 1.34 - 1.45: 4378 1.45 - 1.57: 17210 1.57 - 1.69: 154 1.69 - 1.80: 209 Bond restraints: 32087 Sorted by residual: bond pdb=" CB VAL U 325 " pdb=" CG1 VAL U 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CB VAL O 325 " pdb=" CG1 VAL O 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.53e+00 bond pdb=" CB VAL S 325 " pdb=" CG1 VAL S 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CB VAL M 325 " pdb=" CG1 VAL M 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 bond pdb=" CB VAL I 325 " pdb=" CG1 VAL I 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 32082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 39930 1.18 - 2.37: 2935 2.37 - 3.55: 587 3.55 - 4.74: 147 4.74 - 5.92: 38 Bond angle restraints: 43637 Sorted by residual: angle pdb=" CA TYR O 61 " pdb=" CB TYR O 61 " pdb=" CG TYR O 61 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR K 61 " pdb=" CB TYR K 61 " pdb=" CG TYR K 61 " ideal model delta sigma weight residual 113.90 118.65 -4.75 1.80e+00 3.09e-01 6.96e+00 angle pdb=" CA TYR S 61 " pdb=" CB TYR S 61 " pdb=" CG TYR S 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.93e+00 angle pdb=" CA TYR I 61 " pdb=" CB TYR I 61 " pdb=" CG TYR I 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.92e+00 angle pdb=" CA TYR E 61 " pdb=" CB TYR E 61 " pdb=" CG TYR E 61 " ideal model delta sigma weight residual 113.90 118.63 -4.73 1.80e+00 3.09e-01 6.92e+00 ... (remaining 43632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17412 16.60 - 33.20: 1806 33.20 - 49.80: 263 49.80 - 66.40: 143 66.40 - 83.00: 132 Dihedral angle restraints: 19756 sinusoidal: 8580 harmonic: 11176 Sorted by residual: dihedral pdb=" CA TYR I 59 " pdb=" C TYR I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR G 59 " pdb=" C TYR G 59 " pdb=" N LYS G 60 " pdb=" CA LYS G 60 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR Q 59 " pdb=" C TYR Q 59 " pdb=" N LYS Q 60 " pdb=" CA LYS Q 60 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2884 0.034 - 0.068: 1519 0.068 - 0.102: 546 0.102 - 0.136: 177 0.136 - 0.171: 22 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C1' C P 75 " pdb=" O4' C P 75 " pdb=" C2' C P 75 " pdb=" N1 C P 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" C1' C N 75 " pdb=" O4' C N 75 " pdb=" C2' C N 75 " pdb=" N1 C N 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C1' C D 75 " pdb=" O4' C D 75 " pdb=" C2' C D 75 " pdb=" N1 C D 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 5145 not shown) Planarity restraints: 5291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY S 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLY S 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY S 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS S 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY G 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY G 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY Q 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY Q 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS Q 229 " 0.018 2.00e-02 2.50e+03 ... (remaining 5288 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.36: 121 1.36 - 2.25: 352 2.25 - 3.13: 26184 3.13 - 4.02: 84872 4.02 - 4.90: 156081 Warning: very small nonbonded interaction distances. Nonbonded interactions: 267610 Sorted by model distance: nonbonded pdb=" C3' C J 77 " pdb=" OP1 C L 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C F 77 " pdb=" OP1 C H 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C T 77 " pdb=" OP1 C V 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C R 77 " pdb=" OP1 C T 71 " model vdw 0.481 3.470 nonbonded pdb=" OP1 C B 71 " pdb=" C3' C V 77 " model vdw 0.481 3.470 ... (remaining 267605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 22.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.151 32098 Z= 2.146 Angle : 0.733 5.921 43637 Z= 0.417 Chirality : 0.047 0.171 5148 Planarity : 0.006 0.052 5291 Dihedral : 15.484 82.999 12584 Min Nonbonded Distance : 0.481 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.13), residues: 3817 helix: 1.00 (0.10), residues: 2464 sheet: -1.19 (0.33), residues: 165 loop : -0.11 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 208 TYR 0.027 0.003 TYR E 61 PHE 0.013 0.003 PHE U 214 TRP 0.013 0.002 TRP I 261 HIS 0.003 0.001 HIS U 275 Details of bonding type rmsd covalent geometry : bond 0.00609 (32087) covalent geometry : angle 0.73258 (43637) hydrogen bonds : bond 0.11926 ( 1826) hydrogen bonds : angle 5.93484 ( 5379) Misc. bond : bond 1.15083 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7370 (ttp-110) REVERT: G 138 LEU cc_start: 0.8331 (mp) cc_final: 0.8064 (mp) REVERT: I 53 TYR cc_start: 0.6244 (p90) cc_final: 0.6003 (p90) REVERT: I 138 LEU cc_start: 0.8393 (mp) cc_final: 0.8159 (mp) REVERT: I 249 MET cc_start: 0.7609 (mmm) cc_final: 0.7024 (mmm) REVERT: K 138 LEU cc_start: 0.8610 (mp) cc_final: 0.8360 (mp) REVERT: M 39 SER cc_start: 0.8582 (m) cc_final: 0.8338 (p) REVERT: M 84 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7382 (ttp-110) REVERT: M 249 MET cc_start: 0.7274 (mmm) cc_final: 0.6836 (mmm) REVERT: O 7 HIS cc_start: 0.7683 (t70) cc_final: 0.7453 (t70) REVERT: Q 138 LEU cc_start: 0.8545 (mp) cc_final: 0.8305 (mp) REVERT: S 249 MET cc_start: 0.7544 (mmm) cc_final: 0.7133 (mmm) REVERT: U 39 SER cc_start: 0.8580 (m) cc_final: 0.8319 (p) REVERT: U 138 LEU cc_start: 0.8580 (mp) cc_final: 0.8334 (mp) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1994 time to fit residues: 167.0487 Evaluate side-chains 390 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 148 GLN A 306 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 306 GLN E 80 GLN E 306 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 306 GLN ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 ASN I 80 GLN I 306 GLN ** I 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 306 GLN ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN M 148 GLN M 306 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 148 GLN O 306 GLN ** O 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN Q 148 GLN Q 306 GLN ** Q 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN S 306 GLN ** S 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 306 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138414 restraints weight = 43173.990| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.39 r_work: 0.3398 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32098 Z= 0.155 Angle : 0.590 12.577 43637 Z= 0.309 Chirality : 0.043 0.223 5148 Planarity : 0.007 0.117 5291 Dihedral : 14.066 166.538 5412 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.37 % Allowed : 6.65 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.14), residues: 3817 helix: 1.39 (0.11), residues: 2508 sheet: -0.70 (0.34), residues: 165 loop : -0.12 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 132 TYR 0.023 0.002 TYR C 23 PHE 0.024 0.002 PHE G 348 TRP 0.003 0.001 TRP K 261 HIS 0.007 0.001 HIS O 117 Details of bonding type rmsd covalent geometry : bond 0.00346 (32087) covalent geometry : angle 0.58989 (43637) hydrogen bonds : bond 0.04889 ( 1826) hydrogen bonds : angle 4.58761 ( 5379) Misc. bond : bond 0.00212 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 496 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.5241 (m-80) cc_final: 0.4763 (m-80) REVERT: A 50 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7493 (tp30) REVERT: A 80 GLN cc_start: 0.8825 (tp40) cc_final: 0.8014 (tt0) REVERT: A 249 MET cc_start: 0.7757 (mmm) cc_final: 0.7506 (mmm) REVERT: C 80 GLN cc_start: 0.8920 (tp40) cc_final: 0.8218 (tt0) REVERT: C 115 ASP cc_start: 0.6588 (t70) cc_final: 0.6365 (t70) REVERT: C 249 MET cc_start: 0.7671 (mmm) cc_final: 0.7406 (mmm) REVERT: E 53 TYR cc_start: 0.6887 (p90) cc_final: 0.6550 (p90) REVERT: E 80 GLN cc_start: 0.8803 (tp40) cc_final: 0.8048 (tt0) REVERT: E 290 ASP cc_start: 0.8288 (m-30) cc_final: 0.7999 (m-30) REVERT: E 338 TYR cc_start: 0.7280 (t80) cc_final: 0.7061 (t80) REVERT: G 80 GLN cc_start: 0.8800 (tp40) cc_final: 0.8097 (tt0) REVERT: G 138 LEU cc_start: 0.8510 (mp) cc_final: 0.8142 (mp) REVERT: I 53 TYR cc_start: 0.6595 (p90) cc_final: 0.6062 (p90) REVERT: I 80 GLN cc_start: 0.8841 (tp40) cc_final: 0.8162 (tt0) REVERT: I 115 ASP cc_start: 0.6453 (t70) cc_final: 0.6248 (t70) REVERT: I 138 LEU cc_start: 0.8373 (mp) cc_final: 0.8171 (mp) REVERT: I 151 ARG cc_start: 0.7705 (ptp-170) cc_final: 0.7304 (ptp-170) REVERT: I 249 MET cc_start: 0.7876 (mmm) cc_final: 0.7529 (mmm) REVERT: K 80 GLN cc_start: 0.8953 (tp40) cc_final: 0.8193 (tt0) REVERT: M 80 GLN cc_start: 0.8871 (tp40) cc_final: 0.8098 (tt0) REVERT: M 115 ASP cc_start: 0.6351 (t70) cc_final: 0.5830 (t70) REVERT: O 80 GLN cc_start: 0.8858 (tp40) cc_final: 0.8075 (tt0) REVERT: O 249 MET cc_start: 0.7730 (mmm) cc_final: 0.7460 (mmm) REVERT: Q 80 GLN cc_start: 0.8879 (tp40) cc_final: 0.8102 (tt0) REVERT: Q 138 LEU cc_start: 0.8454 (mp) cc_final: 0.8219 (mp) REVERT: Q 200 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.7086 (mtm-85) REVERT: S 50 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7466 (tp30) REVERT: S 80 GLN cc_start: 0.8960 (tp40) cc_final: 0.8242 (tt0) REVERT: S 249 MET cc_start: 0.7791 (mmm) cc_final: 0.7498 (mmm) REVERT: S 348 PHE cc_start: 0.7957 (t80) cc_final: 0.7614 (t80) REVERT: U 80 GLN cc_start: 0.8834 (tp40) cc_final: 0.8089 (tt0) REVERT: U 138 LEU cc_start: 0.8711 (mp) cc_final: 0.8394 (mp) outliers start: 45 outliers final: 9 residues processed: 507 average time/residue: 0.2279 time to fit residues: 175.9743 Evaluate side-chains 438 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 429 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 10 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 149 optimal weight: 0.0020 chunk 337 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 335 optimal weight: 0.7980 chunk 341 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 284 GLN K 148 GLN M 148 GLN M 284 GLN Q 284 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138854 restraints weight = 42930.550| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.71 r_work: 0.3360 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32098 Z= 0.118 Angle : 0.510 11.324 43637 Z= 0.268 Chirality : 0.038 0.164 5148 Planarity : 0.006 0.206 5291 Dihedral : 14.147 177.002 5412 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.19 % Allowed : 10.77 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.14), residues: 3817 helix: 1.56 (0.11), residues: 2530 sheet: -1.52 (0.31), residues: 209 loop : 0.10 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG U 78 TYR 0.066 0.002 TYR A 23 PHE 0.029 0.002 PHE Q 348 TRP 0.002 0.000 TRP C 261 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00253 (32087) covalent geometry : angle 0.51024 (43637) hydrogen bonds : bond 0.04046 ( 1826) hydrogen bonds : angle 4.26319 ( 5379) Misc. bond : bond 0.00340 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 486 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8627 (tp40) cc_final: 0.7971 (tt0) REVERT: C 23 TYR cc_start: 0.5383 (m-80) cc_final: 0.5058 (m-80) REVERT: C 80 GLN cc_start: 0.8777 (tp40) cc_final: 0.8106 (tt0) REVERT: C 249 MET cc_start: 0.7624 (mmm) cc_final: 0.7319 (mmm) REVERT: C 347 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8010 (mt) REVERT: E 23 TYR cc_start: 0.5167 (m-80) cc_final: 0.4668 (m-80) REVERT: E 80 GLN cc_start: 0.8735 (tp40) cc_final: 0.8026 (tt0) REVERT: E 290 ASP cc_start: 0.8179 (m-30) cc_final: 0.7695 (m-30) REVERT: G 80 GLN cc_start: 0.8685 (tp40) cc_final: 0.8072 (tt0) REVERT: G 138 LEU cc_start: 0.8310 (mp) cc_final: 0.7935 (mp) REVERT: G 249 MET cc_start: 0.7571 (mmm) cc_final: 0.7370 (mmm) REVERT: I 23 TYR cc_start: 0.4995 (m-80) cc_final: 0.4423 (m-80) REVERT: I 53 TYR cc_start: 0.6612 (p90) cc_final: 0.6246 (p90) REVERT: I 80 GLN cc_start: 0.8682 (tp40) cc_final: 0.8071 (tt0) REVERT: I 128 ASP cc_start: 0.7419 (t70) cc_final: 0.7164 (t0) REVERT: I 138 LEU cc_start: 0.8372 (mp) cc_final: 0.8124 (mp) REVERT: K 80 GLN cc_start: 0.8796 (tp40) cc_final: 0.8123 (tt0) REVERT: K 347 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7525 (mm) REVERT: M 23 TYR cc_start: 0.5057 (m-80) cc_final: 0.4803 (m-80) REVERT: M 80 GLN cc_start: 0.8643 (tp40) cc_final: 0.8009 (tt0) REVERT: M 128 ASP cc_start: 0.7731 (t70) cc_final: 0.7394 (t0) REVERT: O 80 GLN cc_start: 0.8691 (tp40) cc_final: 0.7942 (tt0) REVERT: O 128 ASP cc_start: 0.7513 (t70) cc_final: 0.7311 (t0) REVERT: O 249 MET cc_start: 0.7635 (mmm) cc_final: 0.7311 (mmm) REVERT: Q 23 TYR cc_start: 0.4914 (m-80) cc_final: 0.4465 (m-80) REVERT: Q 80 GLN cc_start: 0.8619 (tp40) cc_final: 0.7930 (tt0) REVERT: Q 138 LEU cc_start: 0.8539 (mp) cc_final: 0.8210 (mp) REVERT: Q 346 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7732 (tt0) REVERT: S 80 GLN cc_start: 0.8747 (tp40) cc_final: 0.8125 (tt0) REVERT: S 249 MET cc_start: 0.7465 (mmm) cc_final: 0.7101 (mmm) REVERT: U 80 GLN cc_start: 0.8677 (tp40) cc_final: 0.7999 (tt0) REVERT: U 138 LEU cc_start: 0.8686 (mp) cc_final: 0.8373 (mp) REVERT: U 151 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7191 (ptp-170) REVERT: U 175 THR cc_start: 0.8222 (m) cc_final: 0.8006 (p) outliers start: 39 outliers final: 5 residues processed: 496 average time/residue: 0.2210 time to fit residues: 166.2678 Evaluate side-chains 424 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 416 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 354 optimal weight: 2.9990 chunk 114 optimal weight: 0.0010 chunk 276 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN G 275 HIS G 344 ASN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139126 restraints weight = 42603.657| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.35 r_work: 0.3411 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32098 Z= 0.145 Angle : 0.522 11.868 43637 Z= 0.271 Chirality : 0.039 0.199 5148 Planarity : 0.006 0.162 5291 Dihedral : 14.053 179.097 5412 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 12.57 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.14), residues: 3817 helix: 1.57 (0.11), residues: 2530 sheet: -0.43 (0.36), residues: 165 loop : -0.13 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 78 TYR 0.055 0.002 TYR A 23 PHE 0.028 0.002 PHE C 348 TRP 0.005 0.001 TRP A 261 HIS 0.007 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00330 (32087) covalent geometry : angle 0.52167 (43637) hydrogen bonds : bond 0.04152 ( 1826) hydrogen bonds : angle 4.25757 ( 5379) Misc. bond : bond 0.00347 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 431 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7756 (tp30) cc_final: 0.7433 (tp30) REVERT: A 80 GLN cc_start: 0.8741 (tp40) cc_final: 0.7994 (tt0) REVERT: A 249 MET cc_start: 0.7782 (mmm) cc_final: 0.7364 (mmm) REVERT: C 80 GLN cc_start: 0.8865 (tp40) cc_final: 0.8121 (tt0) REVERT: C 175 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 249 MET cc_start: 0.7851 (mmm) cc_final: 0.7540 (mmm) REVERT: C 347 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7980 (mt) REVERT: E 80 GLN cc_start: 0.8825 (tp40) cc_final: 0.8065 (tt0) REVERT: E 128 ASP cc_start: 0.7589 (t70) cc_final: 0.7338 (t0) REVERT: E 290 ASP cc_start: 0.8302 (m-30) cc_final: 0.7743 (m-30) REVERT: G 80 GLN cc_start: 0.8782 (tp40) cc_final: 0.8144 (tt0) REVERT: G 138 LEU cc_start: 0.8383 (mp) cc_final: 0.7881 (mp) REVERT: I 80 GLN cc_start: 0.8777 (tp40) cc_final: 0.8112 (tt0) REVERT: I 128 ASP cc_start: 0.7551 (t70) cc_final: 0.7293 (t0) REVERT: I 138 LEU cc_start: 0.8160 (mp) cc_final: 0.7866 (mp) REVERT: K 80 GLN cc_start: 0.8891 (tp40) cc_final: 0.8134 (tt0) REVERT: K 347 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7884 (mt) REVERT: M 80 GLN cc_start: 0.8729 (tp40) cc_final: 0.8076 (tt0) REVERT: O 50 GLU cc_start: 0.7663 (tp30) cc_final: 0.7421 (mm-30) REVERT: O 80 GLN cc_start: 0.8773 (tp40) cc_final: 0.8012 (tt0) REVERT: O 249 MET cc_start: 0.7764 (mmm) cc_final: 0.7415 (mmm) REVERT: Q 80 GLN cc_start: 0.8706 (tp40) cc_final: 0.8041 (tt0) REVERT: Q 138 LEU cc_start: 0.8579 (mp) cc_final: 0.8253 (mp) REVERT: S 78 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6785 (tpp-160) REVERT: S 80 GLN cc_start: 0.8826 (tp40) cc_final: 0.8159 (tt0) REVERT: S 249 MET cc_start: 0.7726 (mmm) cc_final: 0.7354 (mmm) REVERT: U 80 GLN cc_start: 0.8774 (tp40) cc_final: 0.8066 (tt0) REVERT: U 113 MET cc_start: 0.4544 (mtp) cc_final: 0.4268 (mtm) REVERT: U 138 LEU cc_start: 0.8617 (mp) cc_final: 0.8229 (mp) REVERT: U 151 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7160 (ptp-170) outliers start: 58 outliers final: 34 residues processed: 452 average time/residue: 0.2406 time to fit residues: 164.8756 Evaluate side-chains 438 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 400 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 358 LEU Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 19 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 3 optimal weight: 0.0010 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 GLN E 275 HIS E 344 ASN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 344 ASN S 148 GLN U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.169645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138232 restraints weight = 42997.214| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.74 r_work: 0.3332 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32098 Z= 0.118 Angle : 0.492 12.166 43637 Z= 0.255 Chirality : 0.038 0.149 5148 Planarity : 0.005 0.114 5291 Dihedral : 14.119 179.095 5412 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.04 % Allowed : 13.27 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.14), residues: 3817 helix: 1.69 (0.11), residues: 2541 sheet: -0.34 (0.37), residues: 165 loop : -0.20 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 78 TYR 0.037 0.001 TYR A 23 PHE 0.030 0.002 PHE I 348 TRP 0.002 0.000 TRP C 261 HIS 0.025 0.001 HIS O 275 Details of bonding type rmsd covalent geometry : bond 0.00262 (32087) covalent geometry : angle 0.49240 (43637) hydrogen bonds : bond 0.03873 ( 1826) hydrogen bonds : angle 4.12805 ( 5379) Misc. bond : bond 0.00168 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 413 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8627 (tp40) cc_final: 0.7965 (tt0) REVERT: A 249 MET cc_start: 0.7575 (mmm) cc_final: 0.7340 (mmm) REVERT: C 80 GLN cc_start: 0.8828 (tp40) cc_final: 0.8137 (tt0) REVERT: C 249 MET cc_start: 0.7681 (mmm) cc_final: 0.7415 (mmm) REVERT: C 347 LEU cc_start: 0.8401 (mm) cc_final: 0.7928 (mt) REVERT: E 80 GLN cc_start: 0.8753 (tp40) cc_final: 0.8118 (tt0) REVERT: E 290 ASP cc_start: 0.8225 (m-30) cc_final: 0.7849 (m-30) REVERT: G 80 GLN cc_start: 0.8739 (tp40) cc_final: 0.8162 (tt0) REVERT: G 138 LEU cc_start: 0.8362 (mp) cc_final: 0.7930 (mp) REVERT: I 80 GLN cc_start: 0.8715 (tp40) cc_final: 0.8056 (tt0) REVERT: I 128 ASP cc_start: 0.7513 (t70) cc_final: 0.7279 (t0) REVERT: I 138 LEU cc_start: 0.8165 (mp) cc_final: 0.7888 (mp) REVERT: I 249 MET cc_start: 0.7629 (mmm) cc_final: 0.7301 (mmm) REVERT: I 344 ASN cc_start: 0.6725 (t0) cc_final: 0.6496 (m-40) REVERT: K 80 GLN cc_start: 0.8762 (tp40) cc_final: 0.8098 (tt0) REVERT: K 347 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7765 (mt) REVERT: M 80 GLN cc_start: 0.8643 (tp40) cc_final: 0.8032 (tt0) REVERT: M 338 TYR cc_start: 0.7039 (t80) cc_final: 0.6719 (t80) REVERT: M 346 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7650 (tt0) REVERT: O 80 GLN cc_start: 0.8702 (tp40) cc_final: 0.8003 (tt0) REVERT: Q 80 GLN cc_start: 0.8705 (tp40) cc_final: 0.8067 (tt0) REVERT: Q 138 LEU cc_start: 0.8561 (mp) cc_final: 0.8227 (mp) REVERT: Q 249 MET cc_start: 0.7668 (mmm) cc_final: 0.7432 (mmm) REVERT: S 78 ARG cc_start: 0.7062 (tpt170) cc_final: 0.6703 (tpp-160) REVERT: S 80 GLN cc_start: 0.8785 (tp40) cc_final: 0.8131 (tt0) REVERT: S 249 MET cc_start: 0.7510 (mmm) cc_final: 0.7209 (mmm) REVERT: U 80 GLN cc_start: 0.8716 (tp40) cc_final: 0.8075 (tt0) REVERT: U 113 MET cc_start: 0.4628 (mtp) cc_final: 0.4198 (mtm) REVERT: U 138 LEU cc_start: 0.8361 (mp) cc_final: 0.7953 (mp) REVERT: U 151 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7223 (ptp-170) outliers start: 67 outliers final: 37 residues processed: 443 average time/residue: 0.2266 time to fit residues: 152.0103 Evaluate side-chains 422 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 383 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 223 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 260 optimal weight: 0.7980 chunk 339 optimal weight: 1.9990 chunk 364 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 GLN E 344 ASN G 148 GLN G 344 ASN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS Q 344 ASN U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136172 restraints weight = 42870.626| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.44 r_work: 0.3318 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32098 Z= 0.196 Angle : 0.574 12.173 43637 Z= 0.294 Chirality : 0.041 0.149 5148 Planarity : 0.006 0.114 5291 Dihedral : 14.090 178.812 5412 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.41 % Allowed : 13.48 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.14), residues: 3817 helix: 1.59 (0.11), residues: 2541 sheet: -0.24 (0.37), residues: 165 loop : -0.27 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 78 TYR 0.031 0.002 TYR A 23 PHE 0.031 0.003 PHE G 348 TRP 0.011 0.001 TRP E 261 HIS 0.007 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00460 (32087) covalent geometry : angle 0.57424 (43637) hydrogen bonds : bond 0.04503 ( 1826) hydrogen bonds : angle 4.33347 ( 5379) Misc. bond : bond 0.00192 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 403 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8532 (tp40) cc_final: 0.7913 (tt0) REVERT: C 80 GLN cc_start: 0.8663 (tp40) cc_final: 0.8081 (tt0) REVERT: C 249 MET cc_start: 0.7725 (mmm) cc_final: 0.7483 (mmm) REVERT: E 80 GLN cc_start: 0.8562 (tp40) cc_final: 0.8002 (tt0) REVERT: E 249 MET cc_start: 0.7922 (mmm) cc_final: 0.7691 (mmm) REVERT: E 275 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.5982 (t-90) REVERT: G 80 GLN cc_start: 0.8538 (tp40) cc_final: 0.8043 (tt0) REVERT: G 138 LEU cc_start: 0.8411 (mp) cc_final: 0.8068 (mp) REVERT: I 128 ASP cc_start: 0.7510 (t70) cc_final: 0.7298 (t0) REVERT: I 249 MET cc_start: 0.7664 (mmm) cc_final: 0.7193 (mmm) REVERT: K 80 GLN cc_start: 0.8672 (tp40) cc_final: 0.8038 (tt0) REVERT: K 347 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7526 (mt) REVERT: M 80 GLN cc_start: 0.8574 (tp40) cc_final: 0.7912 (tt0) REVERT: M 346 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7674 (tt0) REVERT: O 80 GLN cc_start: 0.8585 (tp40) cc_final: 0.7941 (tt0) REVERT: O 249 MET cc_start: 0.7603 (mmm) cc_final: 0.7291 (mmm) REVERT: Q 80 GLN cc_start: 0.8593 (tp40) cc_final: 0.7935 (tt0) REVERT: Q 138 LEU cc_start: 0.8659 (mp) cc_final: 0.8455 (mp) REVERT: S 80 GLN cc_start: 0.8681 (tp40) cc_final: 0.8082 (tt0) REVERT: S 249 MET cc_start: 0.7498 (mmm) cc_final: 0.7205 (mmm) REVERT: U 80 GLN cc_start: 0.8542 (tp40) cc_final: 0.7957 (tt0) REVERT: U 113 MET cc_start: 0.4728 (mtp) cc_final: 0.4282 (mtm) REVERT: U 138 LEU cc_start: 0.8416 (mp) cc_final: 0.8095 (mp) REVERT: U 151 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7259 (ptp-170) outliers start: 79 outliers final: 58 residues processed: 439 average time/residue: 0.2331 time to fit residues: 153.6918 Evaluate side-chains 443 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 382 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 298 optimal weight: 0.4980 chunk 205 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 296 optimal weight: 0.3980 chunk 305 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 329 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 322 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN E 275 HIS I 80 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135957 restraints weight = 43330.185| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.82 r_work: 0.3299 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32098 Z= 0.129 Angle : 0.517 12.970 43637 Z= 0.267 Chirality : 0.038 0.148 5148 Planarity : 0.005 0.125 5291 Dihedral : 14.026 179.156 5412 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.07 % Allowed : 14.89 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.14), residues: 3817 helix: 1.73 (0.11), residues: 2541 sheet: -0.35 (0.35), residues: 165 loop : -0.24 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG Q 78 TYR 0.026 0.001 TYR A 23 PHE 0.033 0.002 PHE C 348 TRP 0.003 0.000 TRP S 261 HIS 0.013 0.001 HIS U 275 Details of bonding type rmsd covalent geometry : bond 0.00289 (32087) covalent geometry : angle 0.51729 (43637) hydrogen bonds : bond 0.03975 ( 1826) hydrogen bonds : angle 4.17762 ( 5379) Misc. bond : bond 0.00260 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8673 (tp40) cc_final: 0.7999 (tt0) REVERT: C 80 GLN cc_start: 0.8855 (tp40) cc_final: 0.8194 (tt0) REVERT: C 249 MET cc_start: 0.7765 (mmm) cc_final: 0.7504 (mmm) REVERT: E 80 GLN cc_start: 0.8758 (tp40) cc_final: 0.8084 (tt0) REVERT: E 249 MET cc_start: 0.7992 (mmm) cc_final: 0.7754 (mmm) REVERT: G 80 GLN cc_start: 0.8728 (tp40) cc_final: 0.8166 (tt0) REVERT: G 138 LEU cc_start: 0.8345 (mp) cc_final: 0.8085 (mp) REVERT: I 80 GLN cc_start: 0.8778 (tp40) cc_final: 0.8019 (tt0) REVERT: I 128 ASP cc_start: 0.7571 (t70) cc_final: 0.7290 (t0) REVERT: I 249 MET cc_start: 0.7779 (mmm) cc_final: 0.7340 (mmm) REVERT: K 80 GLN cc_start: 0.8798 (tp40) cc_final: 0.8115 (tt0) REVERT: K 344 ASN cc_start: 0.6670 (t0) cc_final: 0.5747 (t0) REVERT: K 347 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7659 (mm) REVERT: M 80 GLN cc_start: 0.8698 (tp40) cc_final: 0.7994 (tt0) REVERT: M 338 TYR cc_start: 0.7203 (t80) cc_final: 0.6875 (t80) REVERT: O 80 GLN cc_start: 0.8753 (tp40) cc_final: 0.7994 (tt0) REVERT: Q 80 GLN cc_start: 0.8742 (tp40) cc_final: 0.8127 (tt0) REVERT: Q 138 LEU cc_start: 0.8550 (mp) cc_final: 0.8319 (mp) REVERT: S 80 GLN cc_start: 0.8797 (tp40) cc_final: 0.8134 (tt0) REVERT: S 249 MET cc_start: 0.7541 (mmm) cc_final: 0.7254 (mmm) REVERT: U 80 GLN cc_start: 0.8575 (tp40) cc_final: 0.7935 (tt0) REVERT: U 113 MET cc_start: 0.4788 (mtp) cc_final: 0.4382 (mtm) REVERT: U 138 LEU cc_start: 0.8316 (mp) cc_final: 0.7979 (mp) REVERT: U 151 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7428 (ptp-170) outliers start: 68 outliers final: 54 residues processed: 423 average time/residue: 0.2444 time to fit residues: 156.2523 Evaluate side-chains 432 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 324 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 352 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 348 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 GLN E 275 HIS G 275 HIS I 117 HIS ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135207 restraints weight = 43043.203| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.82 r_work: 0.3289 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32098 Z= 0.138 Angle : 0.537 14.009 43637 Z= 0.274 Chirality : 0.039 0.144 5148 Planarity : 0.005 0.106 5291 Dihedral : 14.071 179.356 5412 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.77 % Allowed : 15.74 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.14), residues: 3817 helix: 1.79 (0.11), residues: 2541 sheet: -0.37 (0.35), residues: 165 loop : -0.22 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Q 78 TYR 0.024 0.001 TYR A 23 PHE 0.034 0.003 PHE M 348 TRP 0.004 0.001 TRP K 261 HIS 0.016 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00317 (32087) covalent geometry : angle 0.53676 (43637) hydrogen bonds : bond 0.03985 ( 1826) hydrogen bonds : angle 4.18812 ( 5379) Misc. bond : bond 0.00217 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 382 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8668 (tp40) cc_final: 0.7970 (tt0) REVERT: A 249 MET cc_start: 0.7675 (tpp) cc_final: 0.7460 (mmm) REVERT: C 80 GLN cc_start: 0.8830 (tp40) cc_final: 0.8107 (tt0) REVERT: C 249 MET cc_start: 0.7757 (mmm) cc_final: 0.7495 (mmm) REVERT: E 80 GLN cc_start: 0.8749 (tp40) cc_final: 0.8067 (tt0) REVERT: E 249 MET cc_start: 0.7990 (mmm) cc_final: 0.7724 (mmm) REVERT: G 80 GLN cc_start: 0.8694 (tp40) cc_final: 0.8139 (tt0) REVERT: G 138 LEU cc_start: 0.8380 (mp) cc_final: 0.8036 (mp) REVERT: I 80 GLN cc_start: 0.8765 (tp40) cc_final: 0.7989 (tt0) REVERT: I 128 ASP cc_start: 0.7564 (t70) cc_final: 0.7315 (t0) REVERT: I 249 MET cc_start: 0.7809 (mmm) cc_final: 0.7357 (mmm) REVERT: K 80 GLN cc_start: 0.8795 (tp40) cc_final: 0.8128 (tt0) REVERT: K 347 LEU cc_start: 0.8415 (mm) cc_final: 0.7843 (mt) REVERT: M 80 GLN cc_start: 0.8681 (tp40) cc_final: 0.8000 (tt0) REVERT: M 84 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7764 (ttp-110) REVERT: M 249 MET cc_start: 0.7828 (tpp) cc_final: 0.7616 (mmm) REVERT: M 338 TYR cc_start: 0.7092 (t80) cc_final: 0.6788 (t80) REVERT: M 346 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7506 (tt0) REVERT: O 80 GLN cc_start: 0.8754 (tp40) cc_final: 0.8001 (tt0) REVERT: O 249 MET cc_start: 0.7626 (mmm) cc_final: 0.7388 (mmm) REVERT: Q 80 GLN cc_start: 0.8760 (tp40) cc_final: 0.8054 (tt0) REVERT: Q 138 LEU cc_start: 0.8583 (mp) cc_final: 0.8325 (mp) REVERT: S 80 GLN cc_start: 0.8815 (tp40) cc_final: 0.8150 (tt0) REVERT: S 249 MET cc_start: 0.7542 (mmm) cc_final: 0.7251 (mmm) REVERT: U 80 GLN cc_start: 0.8572 (tp40) cc_final: 0.7954 (tt0) REVERT: U 113 MET cc_start: 0.4768 (mtp) cc_final: 0.4374 (mtm) REVERT: U 138 LEU cc_start: 0.8283 (mp) cc_final: 0.7932 (mp) REVERT: U 151 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7401 (ptp-170) outliers start: 58 outliers final: 48 residues processed: 409 average time/residue: 0.2570 time to fit residues: 157.9718 Evaluate side-chains 417 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 368 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 116 optimal weight: 0.0170 chunk 169 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 374 optimal weight: 0.5980 chunk 250 optimal weight: 7.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 HIS C 275 HIS E 117 HIS E 275 HIS G 275 HIS I 117 HIS ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136855 restraints weight = 42965.645| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.76 r_work: 0.3345 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32098 Z= 0.112 Angle : 0.522 14.670 43637 Z= 0.264 Chirality : 0.037 0.154 5148 Planarity : 0.005 0.099 5291 Dihedral : 14.063 179.213 5412 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 16.38 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.14), residues: 3817 helix: 1.97 (0.11), residues: 2530 sheet: -0.37 (0.35), residues: 165 loop : -0.24 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG K 78 TYR 0.021 0.001 TYR M 23 PHE 0.033 0.002 PHE M 348 TRP 0.002 0.000 TRP A 123 HIS 0.019 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00246 (32087) covalent geometry : angle 0.52238 (43637) hydrogen bonds : bond 0.03690 ( 1826) hydrogen bonds : angle 4.07796 ( 5379) Misc. bond : bond 0.00207 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 401 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8622 (tp40) cc_final: 0.7921 (tt0) REVERT: A 249 MET cc_start: 0.7686 (tpp) cc_final: 0.7479 (mmm) REVERT: C 80 GLN cc_start: 0.8762 (tp40) cc_final: 0.8097 (tt0) REVERT: C 249 MET cc_start: 0.7672 (mmm) cc_final: 0.7427 (mmm) REVERT: E 80 GLN cc_start: 0.8755 (tp40) cc_final: 0.8059 (tt0) REVERT: E 249 MET cc_start: 0.7926 (mmm) cc_final: 0.7662 (mmm) REVERT: G 80 GLN cc_start: 0.8674 (tp40) cc_final: 0.8117 (tt0) REVERT: G 138 LEU cc_start: 0.8371 (mp) cc_final: 0.8037 (mp) REVERT: G 200 ARG cc_start: 0.7345 (ptp90) cc_final: 0.7012 (mtm-85) REVERT: I 80 GLN cc_start: 0.8741 (tp40) cc_final: 0.8012 (tt0) REVERT: I 249 MET cc_start: 0.7733 (mmm) cc_final: 0.7283 (mmm) REVERT: I 344 ASN cc_start: 0.6469 (t0) cc_final: 0.6175 (t0) REVERT: K 80 GLN cc_start: 0.8698 (tp40) cc_final: 0.7985 (tt0) REVERT: M 80 GLN cc_start: 0.8658 (tp40) cc_final: 0.7991 (tt0) REVERT: M 84 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7753 (ttp-110) REVERT: O 80 GLN cc_start: 0.8736 (tp40) cc_final: 0.7978 (tt0) REVERT: O 249 MET cc_start: 0.7543 (mmm) cc_final: 0.7303 (mmm) REVERT: Q 80 GLN cc_start: 0.8725 (tp40) cc_final: 0.8106 (tt0) REVERT: Q 138 LEU cc_start: 0.8575 (mp) cc_final: 0.8307 (mp) REVERT: Q 249 MET cc_start: 0.7740 (tpt) cc_final: 0.7470 (mmm) REVERT: Q 339 ARG cc_start: 0.7178 (tpp-160) cc_final: 0.6934 (mmt-90) REVERT: S 80 GLN cc_start: 0.8791 (tp40) cc_final: 0.8118 (tt0) REVERT: S 249 MET cc_start: 0.7476 (mmm) cc_final: 0.7216 (mmm) REVERT: U 80 GLN cc_start: 0.8533 (tp40) cc_final: 0.7911 (tt0) REVERT: U 138 LEU cc_start: 0.8286 (mp) cc_final: 0.7937 (mp) REVERT: U 151 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7333 (ptp-170) outliers start: 46 outliers final: 38 residues processed: 426 average time/residue: 0.2249 time to fit residues: 145.5810 Evaluate side-chains 417 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 378 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 182 optimal weight: 0.9990 chunk 382 optimal weight: 0.6980 chunk 153 optimal weight: 0.0040 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 372 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 282 optimal weight: 0.6980 chunk 74 optimal weight: 0.0170 chunk 87 optimal weight: 0.3980 chunk 234 optimal weight: 2.9990 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 117 HIS C 275 HIS E 117 HIS E 275 HIS G 275 HIS I 117 HIS K 250 GLN ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.170164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138365 restraints weight = 43215.182| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.77 r_work: 0.3346 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32098 Z= 0.108 Angle : 0.527 16.280 43637 Z= 0.264 Chirality : 0.037 0.139 5148 Planarity : 0.005 0.097 5291 Dihedral : 14.059 179.525 5412 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.31 % Allowed : 16.75 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.14), residues: 3817 helix: 2.04 (0.11), residues: 2530 sheet: -0.38 (0.35), residues: 165 loop : -0.19 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 78 TYR 0.018 0.001 TYR A 23 PHE 0.033 0.002 PHE M 348 TRP 0.002 0.000 TRP I 261 HIS 0.012 0.001 HIS O 275 Details of bonding type rmsd covalent geometry : bond 0.00237 (32087) covalent geometry : angle 0.52658 (43637) hydrogen bonds : bond 0.03651 ( 1826) hydrogen bonds : angle 4.04337 ( 5379) Misc. bond : bond 0.00192 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8581 (tp40) cc_final: 0.7896 (tt0) REVERT: A 249 MET cc_start: 0.7670 (tpp) cc_final: 0.7455 (mmm) REVERT: C 80 GLN cc_start: 0.8782 (tp40) cc_final: 0.8100 (tt0) REVERT: C 117 HIS cc_start: 0.7808 (t-90) cc_final: 0.7494 (t70) REVERT: C 249 MET cc_start: 0.7702 (mmm) cc_final: 0.7450 (mmm) REVERT: E 80 GLN cc_start: 0.8761 (tp40) cc_final: 0.8066 (tt0) REVERT: E 249 MET cc_start: 0.7927 (mmm) cc_final: 0.7648 (mmm) REVERT: E 339 ARG cc_start: 0.7152 (tpp-160) cc_final: 0.6877 (mmt-90) REVERT: G 80 GLN cc_start: 0.8664 (tp40) cc_final: 0.8106 (tt0) REVERT: G 138 LEU cc_start: 0.8407 (mp) cc_final: 0.8033 (mp) REVERT: G 200 ARG cc_start: 0.7301 (ptp90) cc_final: 0.6978 (mtm-85) REVERT: I 80 GLN cc_start: 0.8707 (tp40) cc_final: 0.7982 (tt0) REVERT: I 249 MET cc_start: 0.7691 (mmm) cc_final: 0.7259 (mmm) REVERT: I 344 ASN cc_start: 0.6435 (t0) cc_final: 0.6146 (t0) REVERT: K 50 GLU cc_start: 0.7900 (tp30) cc_final: 0.7628 (tp30) REVERT: K 80 GLN cc_start: 0.8684 (tp40) cc_final: 0.8051 (tt0) REVERT: K 339 ARG cc_start: 0.7251 (tpp-160) cc_final: 0.6965 (mmt-90) REVERT: M 78 ARG cc_start: 0.7271 (tpt170) cc_final: 0.6777 (tpt170) REVERT: M 80 GLN cc_start: 0.8641 (tp40) cc_final: 0.7989 (tt0) REVERT: M 84 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7765 (ttp-110) REVERT: O 80 GLN cc_start: 0.8731 (tp40) cc_final: 0.8067 (tt0) REVERT: O 249 MET cc_start: 0.7509 (mmm) cc_final: 0.7274 (mmm) REVERT: Q 80 GLN cc_start: 0.8737 (tp40) cc_final: 0.8044 (tt0) REVERT: Q 138 LEU cc_start: 0.8517 (mp) cc_final: 0.8236 (mp) REVERT: S 80 GLN cc_start: 0.8779 (tp40) cc_final: 0.8110 (tt0) REVERT: S 249 MET cc_start: 0.7436 (mmm) cc_final: 0.7188 (mmm) REVERT: U 80 GLN cc_start: 0.8536 (tp40) cc_final: 0.7926 (tt0) REVERT: U 138 LEU cc_start: 0.8251 (mp) cc_final: 0.7899 (mp) outliers start: 43 outliers final: 37 residues processed: 423 average time/residue: 0.2188 time to fit residues: 140.2598 Evaluate side-chains 422 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 385 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 167 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 384 optimal weight: 0.9990 chunk 301 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 383 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS C 344 ASN E 117 HIS E 275 HIS G 275 HIS I 117 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140049 restraints weight = 42786.280| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.35 r_work: 0.3392 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32098 Z= 0.138 Angle : 0.551 16.323 43637 Z= 0.276 Chirality : 0.038 0.134 5148 Planarity : 0.008 0.424 5291 Dihedral : 13.909 179.935 5412 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.40 % Allowed : 16.87 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.14), residues: 3817 helix: 1.98 (0.11), residues: 2530 sheet: -0.36 (0.35), residues: 165 loop : -0.18 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 78 TYR 0.019 0.001 TYR M 23 PHE 0.034 0.002 PHE M 348 TRP 0.004 0.001 TRP K 261 HIS 0.022 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00320 (32087) covalent geometry : angle 0.55137 (43637) hydrogen bonds : bond 0.03823 ( 1826) hydrogen bonds : angle 4.13316 ( 5379) Misc. bond : bond 0.00171 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6773.66 seconds wall clock time: 117 minutes 33.49 seconds (7053.49 seconds total)